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Visualizing the genome: techniques for presenting human genome data and annotations
BACKGROUND: In order to take full advantage of the newly available public human genome sequence data and associated annotations, biologists require visualization tools ("genome browsers") that can accommodate the high frequency of alternative splicing in human genes and other complexities....
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2002
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC119855/ https://www.ncbi.nlm.nih.gov/pubmed/12149135 http://dx.doi.org/10.1186/1471-2105-3-19 |
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author | Loraine, Ann E Helt, Gregg A |
author_facet | Loraine, Ann E Helt, Gregg A |
author_sort | Loraine, Ann E |
collection | PubMed |
description | BACKGROUND: In order to take full advantage of the newly available public human genome sequence data and associated annotations, biologists require visualization tools ("genome browsers") that can accommodate the high frequency of alternative splicing in human genes and other complexities. RESULTS: In this article, we describe visualization techniques for presenting human genomic sequence data and annotations in an interactive, graphical format. These techniques include: one-dimensional, semantic zooming to show sequence data alongside gene structures; color-coding exons to indicate frame of translation; adjustable, moveable tiers to permit easier inspection of a genomic scene; and display of protein annotations alongside gene structures to show how alternative splicing impacts protein structure and function. These techniques are illustrated using examples from two genome browser applications: the Neomorphic GeneViewer annotation tool and ProtAnnot, a prototype viewer which shows protein annotations in the context of genomic sequence. CONCLUSION: By presenting techniques for visualizing genomic data, we hope to provide interested software developers with a guide to what features are most likely to meet the needs of biologists as they seek to make sense of the rapidly expanding body of public genomic data and annotations. |
format | Text |
id | pubmed-119855 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2002 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-1198552002-09-04 Visualizing the genome: techniques for presenting human genome data and annotations Loraine, Ann E Helt, Gregg A BMC Bioinformatics Methodology article BACKGROUND: In order to take full advantage of the newly available public human genome sequence data and associated annotations, biologists require visualization tools ("genome browsers") that can accommodate the high frequency of alternative splicing in human genes and other complexities. RESULTS: In this article, we describe visualization techniques for presenting human genomic sequence data and annotations in an interactive, graphical format. These techniques include: one-dimensional, semantic zooming to show sequence data alongside gene structures; color-coding exons to indicate frame of translation; adjustable, moveable tiers to permit easier inspection of a genomic scene; and display of protein annotations alongside gene structures to show how alternative splicing impacts protein structure and function. These techniques are illustrated using examples from two genome browser applications: the Neomorphic GeneViewer annotation tool and ProtAnnot, a prototype viewer which shows protein annotations in the context of genomic sequence. CONCLUSION: By presenting techniques for visualizing genomic data, we hope to provide interested software developers with a guide to what features are most likely to meet the needs of biologists as they seek to make sense of the rapidly expanding body of public genomic data and annotations. BioMed Central 2002-07-30 /pmc/articles/PMC119855/ /pubmed/12149135 http://dx.doi.org/10.1186/1471-2105-3-19 Text en Copyright ©2002 Loraine and Helt; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. |
spellingShingle | Methodology article Loraine, Ann E Helt, Gregg A Visualizing the genome: techniques for presenting human genome data and annotations |
title | Visualizing the genome: techniques for presenting human genome data and annotations |
title_full | Visualizing the genome: techniques for presenting human genome data and annotations |
title_fullStr | Visualizing the genome: techniques for presenting human genome data and annotations |
title_full_unstemmed | Visualizing the genome: techniques for presenting human genome data and annotations |
title_short | Visualizing the genome: techniques for presenting human genome data and annotations |
title_sort | visualizing the genome: techniques for presenting human genome data and annotations |
topic | Methodology article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC119855/ https://www.ncbi.nlm.nih.gov/pubmed/12149135 http://dx.doi.org/10.1186/1471-2105-3-19 |
work_keys_str_mv | AT loraineanne visualizingthegenometechniquesforpresentinghumangenomedataandannotations AT heltgregga visualizingthegenometechniquesforpresentinghumangenomedataandannotations |